                                           :options  [["-h" "--help" "Show help" :default false :flag true]]
                                           :commands [["view"    "Extract/print all or sub alignments in SAM or BAM format."]
                                                      ["convert" "Convert SAM to BAM or BAM to SAM."]
+                                                     ["normalize" "Normalize references of alignments"]
                                                      ["sort"    "Sort alignments by leftmost coordinates."]
                                                      ["index"   "Index sorted alignment for fast random access."]
                                                      ["pileup"  "Generate pileup for the BAM file."]

                   [io :as io]
                   [bam :as bam]
                   [bam-indexer :as bai]
                   [sorter :as sorter]
                   [fasta :as fa]
                   [fasta-indexer :as fai]

    (case cmd
      :view    (view args)
      :convert (convert args)
      :normalize (normalize args)
      :sort    (sort args)
      :index   (index args)
      :pileup  (pileup args)
